This perspective describes predictive processing as a computational framework for understanding cortical function in the context of emerging evidence, with a focus on sensory processing. We discuss ...how the predictive processing framework may be implemented at the level of cortical circuits and how its implementation could be falsified experimentally. Lastly, we summarize the general implications of predictive processing on cortical function in healthy and diseased states.
In this perspective, Keller and Mrsic-Flogel describe the advantages of predictive processing as a computational framework for understanding cortical function in the context of emerging evidence with a focus on sensory processing.
A major issue in ecology, biogeography, conservation biology and invasion biology is the extent to which climate, and hence climate change, contributes to the positions of species' range boundaries. ...Thirty years of rapid climate warming provides an excellent opportunity to test the hypothesis that climate acts as a major constraint on range boundaries, treating anthropogenic climate change as a large-scale experiment. UK and global data, and literature. This article analyses the frequencies with which species have responded to climate change by shifting their range boundaries. It does not consider abundance or other changes. For the majority of species, boundaries shifted in a direction that is concordant with being a response to climate change; 84% of all species have expanded in a polewards direction as the climate has warmed (for the best data available), which represents an excess of 68% of species after taking account of the fact that some species may shift in this direction for non-climatic reasons. Other data sets also show an excess of animal range boundaries expanding in the expected direction. Climate is likely to contribute to the majority of terrestrial and freshwater range boundaries. This generalization excludes species that are endemic to specific islands, lakes, rivers and geological outcrops, although these local endemics are not immune from the effects of climate change. The observed shifts associated with recent climate change are likely to have been brought about through both direct and indirect (changes to species' interactions) effects of climate; indirect effects are discussed in relation to laboratory experiments and invasive species. Recent observations of range boundary shifts are consistent with the hypothesis that climate contributes to, but is not the sole determinant of, the position of the range boundaries of the majority of terrestrial animal species.
Toll-like receptors (TLRs) are transmembrane pattern recognition receptors that are best known for their roles in innate immunity for the detection of and defense against microbial pathogens. ...However, TLRs also have roles in many nonimmune processes, most notably development. TLRs direct both immune and developmental programs by activation of downstream signaling pathways, often by activation of the NF-κB pathway. There are two primary TLR subtypes: 1) TLRs with multiple cysteine clusters in their ectodomain (mccTLRs) and 2) TLRs with a single cysteine cluster in their ectodomain (sccTLRs). For some time, it has been known that TLRs and the biological processes that they control are conserved in organisms from insects to mammals. However, genome and transcriptome sequencing has revealed that many basal metazoans also have TLRs and downstream NF-κB signaling components. In this review, we discuss what is known about the structure, biological function, and downstream signaling pathways of TLRs found in phyla from Porifera through Annelida. From these analyses, we hypothesize that mccTLRs emerged in the phylum Cnidaria, that sccTLRs evolved in the phylum Mollusca, and that TLRs have dual immune and developmental biological functions in organisms as ancient as cnidarians.
Many of the species at greatest risk of extinction from anthropogenic climate change are narrow endemics that face insurmountable dispersal barriers. In this review, I argue that the only viable ...option to maintain populations of these species in the wild is to translocate them to other locations where the climate is suitable. Risks of extinction to native species in destination areas are small, provided that translocations take place within the same broad geographic region and that the destinations lack local endemics. Biological communities in these areas are in the process of receiving many hundreds of other immigrant species as a result of climate change; ensuring that some of the ‘new’ inhabitants are climate-endangered species could reduce the net rate of extinction.
It is unknown if adult human skeletal muscle has an epigenetic memory of earlier encounters with growth. We report, for the first time in humans, genome-wide DNA methylation (850,000 CpGs) and gene ...expression analysis after muscle hypertrophy (loading), return of muscle mass to baseline (unloading), followed by later hypertrophy (reloading). We discovered increased frequency of hypomethylation across the genome after reloading (18,816 CpGs) versus earlier loading (9,153 CpG sites). We also identified AXIN1, GRIK2, CAMK4, TRAF1 as hypomethylated genes with enhanced expression after loading that maintained their hypomethylated status even during unloading where muscle mass returned to control levels, indicating a memory of these genes methylation signatures following earlier hypertrophy. Further, UBR5, RPL35a, HEG1, PLA2G16, SETD3 displayed hypomethylation and enhanced gene expression following loading, and demonstrated the largest increases in hypomethylation, gene expression and muscle mass after later reloading, indicating an epigenetic memory in these genes. Finally, genes; GRIK2, TRAF1, BICC1, STAG1 were epigenetically sensitive to acute exercise demonstrating hypomethylation after a single bout of resistance exercise that was maintained 22 weeks later with the largest increase in gene expression and muscle mass after reloading. Overall, we identify an important epigenetic role for a number of largely unstudied genes in muscle hypertrophy/memory.
Proton transfer through the water gossamer Hassanali, Ali; Giberti, Federico; Cuny, Jérôme ...
Proceedings of the National Academy of Sciences - PNAS,
08/2013, Volume:
110, Issue:
34
Journal Article
Peer reviewed
Open access
The diffusion of protons through water is understood within the framework of the Grotthuss mechanism, which requires that they undergo structural diffusion in a stepwise manner throughout the water ...network. Despite long study, this picture oversimplifies and neglects the complexity of the supramolecular structure of water. We use first-principles simulations and demonstrate that the currently accepted picture of proton diffusion is in need of revision. We show that proton and hydroxide diffusion occurs through periods of intense activity involving concerted proton hopping followed by periods of rest. The picture that emerges is that proton transfer is a multiscale and multidynamical process involving a broader distribution of pathways and timescales than currently assumed. To rationalize these phenomena, we look at the 3D water network as a distribution of closed directed rings, which reveals the presence of medium-range directional correlations in the liquid. One of the natural consequences of this feature is that both the hydronium and hydroxide ion are decorated with proton wires. These wires serve as conduits for long proton jumps over several hydrogen bonds.
The data and tools in PANTHER-a comprehensive, curated database of protein families, trees, subfamilies and functions available at http://pantherdb.org-have undergone continual, extensive improvement ...for over a decade. Here, we describe the current PANTHER process as a whole, as well as the website tools for analysis of user-uploaded data. The main goals of PANTHER remain essentially unchanged: the accurate inference (and practical application) of gene and protein function over large sequence databases, using phylogenetic trees to extrapolate from the relatively sparse experimental information from a few model organisms. Yet the focus of PANTHER has continually shifted toward more accurate and detailed representations of evolutionary events in gene family histories. The trees are now designed to represent gene family evolution, including inference of evolutionary events, such as speciation and gene duplication. Subfamilies are still curated and used to define HMMs, but gene ontology functional annotations can now be made at any node in the tree, and are designed to represent gain and loss of function by ancestral genes during evolution. Finally, PANTHER now includes stable database identifiers for inferred ancestral genes, which are used to associate inferred gene attributes with particular genes in the common ancestral genomes of extant species.
The year 2024 marks 70 years since the general outline of the carbon pathway in photosynthesis was published. Although several alternative pathways are now known, it is remarkable how many organisms ...use the reaction sequence described 70 yrs ago, which is now known as the Calvin-Benson cycle or variants such as the Calvin-Benson-Bassham cycle or Benson-Calvin cycle. However, once the carbon has entered the Calvin-Benson cycle and is converted to a 3-carbon sugar, it has many potential fates. This review will examine the last stages of photosynthetic metabolism in leaves. In land plants, this process mostly involves the production of sucrose provided by an endosymbiont (the chloroplast) to its host for use and transport to the rest of the plant. Photosynthetic metabolism also usually involves the synthesis of starch, which helps maintain respiration in the dark and enables the symbiont to supply sugars during both the day and night. Other end products made in the chloroplast are closely tied to photosynthetic CO2 assimilation. These include serine from photorespiration and various amino acids, fatty acids, isoprenoids, and shikimate pathway products. I also describe 2 pathways that can short circuit parts of the Calvin-Benson cycle. These final processes of photosynthetic metabolism play many important roles in plants.
Abstract
PANTHER (Protein Analysis Through Evolutionary Relationships, http://www.pantherdb.org) is a resource for the evolutionary and functional classification of protein-coding genes from all ...domains of life. The evolutionary classification is based on a library of over 15,000 phylogenetic trees, and the functional classifications include Gene Ontology terms and pathways. Here, we analyze the current coverage of genes from genomes in different taxonomic groups, so that users can better understand what to expect when analyzing a gene list using PANTHER tools. We also describe extensive improvements to PANTHER made in the past two years. The PANTHER Protein Class ontology has been completely refactored, and 6101 PANTHER families have been manually assigned to a Protein Class, providing a high level classification of protein families and their genes. Users can access the TreeGrafter tool to add their own protein sequences to the reference phylogenetic trees in PANTHER, to infer evolutionary context as well as fine-grained annotations. We have added human enhancer-gene links that associate non-coding regions with the annotated human genes in PANTHER. We have also expanded the available services for programmatic access to PANTHER tools and data via application programming interfaces (APIs). Other improvements include additional plant genomes and an updated PANTHER GO-slim.
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